Salient Characteristics.docx

Salient Characteristics Real-time PCR applications Real-time PCR is very flexible and can be used for the following applications:

• Gene expression analysis

• Genotyping

• Copy number variation analysis

• Pathogen detection, strain typing, and viral load determination

• miRNA profiling

• Protein analysis with proximity ligation assays

• Quality control for detection of environmental contaminants

• Biofuel development

• The ability to monitor the progress of the PCR run as it occurs in real time (on both the instrument touchscreen and software client)

• The ability to accurately measure the amount of amplicon at each cycle

• An increased dynamic range of detection compared to other nucleic acid detection methods

• The combination of amplification and detection in a single tube, eliminating post-PCR manipulations

1. The system utilizes the Connect platform (providing up to 1 TB of storage space) for data sharing at the user’s discretion.

2. The system can be used with online scientific analysis apps available through the Connect platform.

3. The system comes with desktop-based software, allowing for run setup, single-plate analysis, and multi-plate study.

Instrument

4. The instrument comes in one of three fixed-block options: 96-well (0.1 mL), 96-well (0.2 mL), or 384-well. All block options have the capacity to run Fast protocols and complete runs in <30 minutes (96-well) or 35 minutes (384-well).

5. The instrument does not require a field service engineer (FSE) visit for installation and can be set up by the end user directly out of the box. An IT checklist is provided to streamline Internet connectivity.

6. The instrument can be installed without a need for a computer.

7. The instrument installation includes an optional RNase P verification plate to run in order to verify performance.

8. Instrument installation does not require dye calibration.

9. The instrument’s block is accessible from the front of the instrument to maximize bench space, and is fully motorized.

10. The instrument’s dimensions are 27 x 50 x 40 cm (W x D x H), designed to maximize horizontal and vertical bench space.

11. The instruments with a 96-well block are designed to analyze 96 samples simultaneously in any of the following formats: 96-well plate with optical adhesive cover, 96-well plate with optical flat caps, 8-tube strips with optical flat caps, or individual tubes with optical flat caps.

12. The 96-well sample block is made up of at least 6 separate Peltier elements (known as VeriFlex Blocks). The maximum temperature difference that can be programmed across the block is 25°C. The maximum difference in temperature allowed between adjacent blocks is 5°C.

13. The instrument is designed to support reaction volumes of 10–30 μL on the 0.1 mL 96-well block, 10–100 μL on the 0.2 mL 96-well block, and 5–20 μL on the 384-well block.

14. The instrument is factory calibrated with FAM™, SYBR™ Green I, VIC™, NED™, ABY™, JUN™, Mustang Purple™, TAMRA™, Cy®5, and ROX™ dyes.

15. Melt or dissociation curves take place in steps with ΔT varying between 0.015°C and 3.66°C.

16. The instrument has a maximum block ramp rate of 6.5°C/sec for the 0.2 mL 96-well block, 9.0°C/sec for the 0.1 mL 96-well block, and 6.0°C/sec for the 384-well block.

17. The instrument block has a temperature range of 4–99.9ºC.

18. The instrument heated cover has a temperature range of 50 –110ºC.

19. The instrument includes a long-lasting bright white LED (light-emitting diode) source that has a median lifetime of at least 60,000 hours.

20. The instrument uses a CMOS imager for data acquisition to collect data for each filter combination in <2 seconds.

21. The instrument can be used with 100–240 V outlets without modification or special plug requirements.

22. The instrument includes a heated lid assembly that heats the top of the sample plates and provides an effective seal to minimize evaporation of the reaction mixture.

Instrument onboard computer

23. The instrument can run in stand-alone mode, without a computer attached.

24. The instrument includes a touchscreen interface and can store protocols for quick run starts from the instrument without the need for a computer.

25. The instrument’s touchscreen interface enables viewing of amplification plots and filtering by sample, target, and task.

26. The instrument’s touchscreen interface facilitates uploading of protocols or downloading of run files using a USB connection, local area network, and the Connect platform.

27. The instrument’s touchscreen interface facilitates uploading of protocols or run files directly to the Connect platform.

28. The instrument contains onboard storage capability with memory capacity of 10 GB for storing between 1,000 and 5,000 standard absolute quantification run files, and is designed for run protection in case of network or power outages.

29. The instrument can be customized, through the touchscreen, for time zone and service/calibration notification settings.

30. The instrument’s touchscreen interface allows for creation of local user accounts with PIN-protected access. Individual user accounts for the Connect platform can be linked to online accounts on thermofisher.com.

31. The instrument’s touchscreen interface allows users to create and run protocols as guests.

32. The instrument’s touchscreen interface allows for editing of thermal protocols, including editing of individual PCR stages, individual PCR steps, VeriFlex™ Block settings, Auto Delta settings, programmable pause settings, temperature settings, step duration settings, reaction volume settings, heated cover temperature, and ramp rate settings.

33. The instrument’s touchscreen interface allows users to load template (.edt) files from a USB drive, local area network, or the Connect platform.

34. The instrument’s touchscreen interface allows users to designate a destination for completed run files and Cq export to a USB drive, local area network, or the Connect platform.

35. The instrument’s touchscreen interface allows user to enter reagent information into the run file, including reagent name, barcode, type, catalog number, lot number, and expiration date. An optional 2D barcode reader allows automatic entry of this information from Applied Biosystems™ reagents labeled with compatible 2D barcodes.

36. The instrument’s touchscreen interface allows a run in progress to be paused. The user can set the block temperature during the run pause. During the pause, the user can open/close the block drawer to access samples. From the touchscreen, the user can resume the run from the point at which it was paused.

37. The instrument’s touchscreen interface allows users to edit sample and target assignments.

38. The instrument’s touchscreen interface allows users to repeat a previous run.

39. The instrument’s touchscreen interface allows users to perform dye calibrations and view results on the touchscreen.

40. The instrument’s touchscreen interface allows users to perform an RNase P verification plate run and automatically provides pass/fail results.

41. The instrument’s touchscreen interface allows user to back up and restore data and settings.

42. The instrument’s touchscreen interface allows user to run a self-verification test.

43. The instrument’s touchscreen interface allows users to view the curve QC assessment upon calibration and RNase P plate run completion.

44. The instrument’s touchscreen allows users to monitor the run in progress and receive email notifications for run status.

Performance

45. The instrument is designed to complete a 40-cycle real-time PCR run using a fluorogenic 5ʹ nuclease assay and Fast chemistry in a standard 96-well plate in under 30 minutes. The instrument can also run in standard ramping mode with standard chemistry.

46. The instrument includes an OptiFlex system that combines six decoupled excitation and emission filter sets to enable collection of up to 21 unique combinations of wavelengths during a single run for multiplexing on the 96-well block instrument.

47. The instrument includes an OptiFlex system that combines five coupled excitation and emission filter sets to enable collection of up to five unique combinations of wavelengths during a single run for multiplexing on the 384-well block instrument.

48. The instrument supports at least two reaction chemistries, the fluorogenic 5ʹ nuclease assay using Applied Biosystems™ TaqMan® probes, and the DNA-binding chemistry of Applied Biosystems™ SYBR™ Green dye.

49. The instrument has real-time quantitative PCR installation specifications to demonstrate the ability to distinguish 5,000 template copies from 10,000 copies at a 99.7% confidence level.

Software

50. The instrument software allows flexible customization of run protocols.

51. The instrument software allows the creation of secure templates that are locked with a password to limit modification of the run setup.

52. The instrument online software provides run monitoring of connected instruments.

53. The instrument software includes preoptimized run protocols for applications like standard curve, relative standard curve, relative quantification, gene expression, and single-nucleotide polymorphism (SNP) genotyping, with both TaqMan and SYBR Green assay chemistries, for quick starts of runs.

54. The Connect platform is supported by Chrome™, Internet Explorer™, Firefox™, and Safari™ browsers.

55. The instrument includes a copy of free software that is designed to analyze the fluorescence data for the applications of absolute quantification, relative quantification, presence/absence assays, and allelic discrimination/SNP detection.

56. The instrument software collects information on both TaqMan and SYBR Green assay chemistries in the same run by collecting different filter colors for PCR vs. melt curve stages.

57. The instrument software contains a genotyping optimization tool that uses real-time data to help pick the best cycle number for the genotyping call, which helps save run cycles and time.

58. The instrument software provides raw fluorescence data and multicomponent data (segregated by dye type) for troubleshooting of experiments.

59. The instrument online software allows conversion of protocols for the Applied Biosystems™ StepOnePlus™ and 7500 instruments to system protocols.

60. The instrument online software allows users to batch-analyze up to 500 experiments simultaneously.

61. The instrument software can control the instrument and analyze the instrument’s data from a remote computer on the same network.

62. The instrument online software provides status monitoring of connected instruments and real-time run plots.

63. The instrument online software can send user notifications via email or text message when a run is started, stopped, or has reached an error state.

64. The instrument online software provides fast access to completed runs from any connected instrument.

65. The instrument online software will allow registered users of the Connect platform to monitor any connected instrument using a compatible browser.

66. The instrument software is designed to allow users to run an assay plate without performing plate setup prior to beginning the run, and to correct all plate setup mistakes after the run, including incorrect dye or target assignment.

67. The instrument software is designed to export all run results including raw and analyzed data, to a Microsoft™ Excel™ sheet, and save all graphs as .jpg files.

68. The instrument online software provides the ability to import a standard curve from one plate for analysis of another plate of the same instrument type.

69. The instrument online software provides an endogenous control selection tool for gene expression experiments.

70. Instrument online software includes statistical analysis tools like box-whisker plots to assess Ct distribution, and scatter plots and heat maps to assess sample correlation and quality.

71. The instrument software allows users to preselect which data to export and the location of the exported file.

72. The instrument software allows for command-line functions for batch exporting of analyzed run files.

73. The instrument software allows users to save predefined analysis settings for auto-exporting run data into their format of choice, including Applied Biosystems™ 7900HT software, ViiA™ 7 software, and RDML (real-time data markup language, compliant with MIQE guidelines) formats.

74. The instrument desktop software includes a security and auditing module that facilitates 21 CFR Part 11 compliance.

75. The instrument software contains an optional online high-resolution melt (HRM) application that allows users to specify the number of clusters/variants and save their defined controls and analysis settings.

76. Optional primer and probe design software is available for purchase.

Instrument ecosystem

77. The instrument is part of a desktop ecosystem that consists of a suite of qPCR applications. Instrument data can be grouped (multi-plate) for relative quantitation, SNP genotyping, standard curve, high-resolution protein melt, and presence/absence analysis.

78. The instrument is part of the Connect platform that consists of a suite of qPCR analysis modules. Instrument data can be grouped (multi-plate) for relative quantitation, SNP genotyping, standard curve, high-resolution protein melt, and presence/absence analysis.

79. The instrument can optionally be connected to the Connect platform where run setup can be downloaded, and instrument data can be uploaded automatically and shared with other authorized users of Connect.

80. A connected instrument run can be monitored in real time via a web browser or mobile device.

81. The online relative quantitation module allows users to batch-analyze up to 500 experiments simultaneously.

82. Both the desktop and online relative quantitation software provide an endogenous control selection tool for gene expression experiments.

83. Both the desktop and online relative quantitation software include statistical analysis tools like box-whisker plots to assess Ct distribution, and scatter plots and heat maps to assess sample correlation and quality. The online standard curve module provides the ability to apply standard curve metrics from another plate.

84. Both the desktop and online genotyping software contain a genotyping optimization tool that uses real-time data to help pick the best cycle number for the genotyping call, which helps save run cycles and time.

85. Both the desktop and online HRM software allow the user to specify the number of clusters/variants and save their defined controls and analysis settings.

Design

86. An application programming interface (API) is included that will allow programming routines to be developed for controlling the instrument.

87. The instrument is cUL (tested to CAN/CSA standards), UL, CE, C-TICK, WEEE compliant.

88. The instrument is developed and manufactured in a facility with quality system requirements that comply with ISO 13485 standards and ISO 9001 standards.

Gene expression profiling

89. For gene expression profiling, users can select from more than 61,000 predesigned human, mouse, and rat Applied Biosystems™ TaqMan® Assays.

Vendor service and support

90. The instrument is provided with a limited warranty for a period of one year from the date of installation (or 15 months from the date of shipment—whichever is earlier). Optional post-warranty service contracts that include next business day on-site repairs are available.

91. The instrument is provided with an orientation session by eLearning module or a trained technical scientist.

92. The vendor can supply all the necessary consumables to perform instrument qualification (IQ), operational qualification (OQ), and instrument performance verification (IPV).

93. The vendor can provide computer system validation consulting services with flexible and comprehensive audit-style documentation packages that help users reduce risk and comply with regulations and standards.

94. The vendor offers telephone technical support and field applications, sales, and service support to help resolve chemistry and instrumentation problems.